Re: [AMBER] Non-polar solvation free energy in AMBER11

From: Ray Luo, Ph.D. <>
Date: Fri, 12 Oct 2012 10:25:22 -0700

Hi Tong,

It seems that your output files are complete. Are these output files from
Amber11? Also, you were not using inp=2 in Amber11, so it ran well. In
Amber12, you might have set inp=2 and that's why it failed.


On Thu, Oct 11, 2012 at 11:45 PM, Tong Zhu <> wrote:

> Dear Prof. Luo,
> Thank you so much for your help!
> The detail input and parameter files used in my calculation is attached.
> In this calculation, I used in AMBER11, and it works, however,
> when I switch to AMBER12, nothing will be output.
> I find that the PTRAJ module is used in AMBER11 while the CPPTRAJ is used
> in AMBER12, does the error caused by this difference?
> All the best~~
> Tong
> Dear Tong,
> One thing to keep in mind is that inp=2, i.e. the approach separating
> the nonpolar solvation energy into the dispersion and cavity terms,
> only works for standard Amber atom types, i.e. those in upper cases,
> not those with GAFF types ...
> I'm not sure whether your error was due to this. If you want, please
> email me, off the list, your detailed input, prmtop, and output files,
> so we can take a look.
> All the best,
> Ray
> On Wed, Oct 10, 2012 at 11:55 PM, Tong Zhu<> wrote:
> Dear everyone,
>> Thank you very much for your time. I have a protein-ligand structure in
>> which the ligand are coordinate with a zinc ion in the protein, and I
>> want to calculated the binding free energy of this system. I have both
>> AMBER12 and AMBER11.
>> However, strangely, the in AMBER11 can work with this
>> structure, but which in AMBER12 can not, Would you please give me some
>> advice to find the reasons?
>> The error information of amber 12 is :
>> Reading command-line arguments and input files...
>> Loading and checking parameter files for compatibility...
>> ValueError: unsupported format character 'V' (0x56) at index 10
>> Exiting. All files have been retained.
>> I addition, If I use AMBER11 in my calculation, how can I use the
>> (INP=2) option? I want the non-polar solvation free energy is modeled as
>> two terms: the cavity term and the dispersion term.
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Received on Fri Oct 12 2012 - 10:30:02 PDT
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